Installation of genomes or partial genomes into cells or cell-like systems

ABSTRACT

A method is provided for introducing a genome into a cell or cell-like system. The introduced genome may occur in nature, be manmade with or without automation, or may be a hybrid of naturally occurring and manmade materials. The genome is obtained outside of a cell with minimal damage. Materials such as a proteins, RNAs, polycations, nucleoid condensation proteins, or gene translation systems may accompany the genome. The genome is installed into a naturally occurring cell or into a manmade cell-like system. A cell-like system or synthetic cell resulting from the practice of the provided method may be designed and used to yield gene-expression products, such as desired proteins. By enabling the synthesis of cells or cell-like systems comprising a wide variety of genomes, accompanying materials and membrane types, the provided method makes possible a broader field of experimentation and bioengineering than has been available using prior art methods.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims benefit and priority from U.S.Provisional Patent Application Ser. No. 60/752,965 filed on Dec. 23,2005, Attorney Docket #40921-226812 entitled, “Introduction of Genomesinto Microorganisms,” which is herein incorporated by reference.

This invention was made with government support (DOE grant no.DE-FG02-02ER63453). The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates generally to cell biology, and moreparticularly to the synthesis of cells or cell-like systems.

2. Description of Related Art

Methods of altering cellular genomes and membranes are useful fortesting hypotheses in the field of cell biology, as well as for thebioengineering of cell models, designer cells and organisms withtailored genomes. One recent approach to designing or altering cells isknocking out genes from bacterial cells to obtain cells with genomesthat are smaller than the naturally occurring genome, which nonethelessremain capable of certain functions, such as reproduction. While suchapproaches afford some ability to learn about genomic function anddesign, approaches that enable fuller control over the contents ofgenomes, cell membranes and cell volumes will yield scientific andtechnological advances through superior experimental control andbioengineering capability.

What is desired is a method for synthesizing cells or cell-like systemsso that a desired genome may be installed into a target cell, vesicle orother membrane-bound volume. An approach that allows the use of anygenome, whether naturally occurring, manmade, or a hybrid of natural andmanmade nucleic acid sequences, allows for the tailoring of the cellularand genomic environment, such as the inclusion or exclusion of materialson various scales (for example, small molecules, proteins, and/orribosomes or nucleic acid translation and/or transcription systems), andallows for the design of the cellular membrane (again, drawing fromnaturally occurring membranes, manmade materials capable of formingaqueous compartments, or hybrids of such membranes and materials) willopen vast horizons of genomic and cellular experimentation and design tobasic research and biotechnological development.

SUMMARY OF THE INVENTION

A method is provided for installing a genome into a cell or cell-likesystem. The installed or introduced genome may occur in nature, bemanmade with or without automation, or may be a hybrid of naturallyoccurring and manmade materials. The delicate genome is obtained outsideof a cell with minimal damage. Materials that stabilize the genome orotherwise make it amenable to transfer into recipient cells or cell-likesystems such as proteins, RNAs, polycations, or even systems as in agene translation system, may accompany the genome. Some of the DNAnucleotides of the genome may be methylated or otherwise modified tomake the genome more resemble a natural chromosome. The genome may berelaxed, supercoiled or even linearized if the normal configuration iscircular. The genome is introduced into a naturally occurring cell orinto a manmade cell-like system, such as a lipid vesicle or a ghost cellfrom which the naturally occurring genome has been suppressed oreliminated. A cell-like system or synthetic cell resulting from thepractice of the provided method may be designed and used to yieldgene-expression products, such as desired proteins, or to produce anovel manmade bacterial species whose designed genome makes it capableof extraordinary activities that are not performed by any natural cell,such as synthesizing peptides comprised of other than the standard 20amino acids. By enabling the synthesis of cells or cell-like systemscomprising a wide variety of genomes, accompanying materials andmembrane types, the provided method makes possible a broader field ofexperimentation and bioengineering than has been available using priorart methods.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a diagram illustrating an exemplary method for installing agenome or partial genome into a cell or cell-like system.

FIG. 2 is a diagram illustrating an exemplary method for installing agenome or partial genome comprising supercoiled DNA, scaffoldingproteins and ribosomes (not to scale) into an E. coli cell that stillcontains its naturally occurring genome.

FIG. 3 is a diagram illustrating an exemplary method for producing agene-expression product of interest using one or more synthetic cells.

DETAILED DESCRIPTION OF THE INVENTION

The ability to design a cell or cell-like system, including the genome,the membrane and the cytoplasm or membrane-bound aqueous volume, isparticularly valuable in the fields of cell biology and biotechnology.

Embodiments of the present invention provide a method for synthesizing acell or cell-like system. A “cell-like system” is a system thatresembles a naturally occurring cell, but does not occur without humanintervention. Cell-like systems include mammalian red blood cells(mammalian red blood cells do not naturally contain a genome) into whicha genome or partial genome has been installed (or “introduced”), a“ghost cell” into which a genome has been introduced, an aqueous volumeenclosed by a phospholipid bilayer (whether derived from a naturallyoccurring cell membrane, manmade, or a hybrid of naturally occurring andmanmade components) into which a genome has been introduced, and anaqueous volume enclosed by a lipid vesicle into which a genome has beenintroduced. A ghost cell is a cell that naturally encloses a genome, butfrom which the naturally occurring genome is absent either as a resultof genetic programming causing some cells to be genome-free or becausethe genome has been removed or inactivated. A partial genome comprisesone or more chromosomes or chromosome fragments. For example, a partialgenome may be any fraction of a naturally occurring genome, one or morefragments of one or more naturally occurring chromosomes, or one or morefragments of one or more naturally occurring chromosomes and one or moremanmade nucleic acid sequences, one or more manmade nucleic acidsequences or fragments of manmade nucleic acid sequences, etc.

Ghost cells may be produced by any means, including but not limited tophysical methods such ultraviolet and gamma irradiation, genetic methodsinvolving minicells, and treatment with chemical compounds such asantibiotics and peroxides. In an exemplary embodiment, the naturallyoccurring genomes are removed from a cell of Mycoplasma pneumoniae and acell of Mycoplasma genitalium, and the M. genitalium genome isintroduced into the M. pneumoniae ghost cell. In some embodiments, ghostcells are produced from M. alligatoris and/or M. capricolum. Becauseboth of these grow rapidly, their use yields results more quickly thanthat of M. genitalium, which takes three weeks to form a microscopiccolony, or M. pneumoniae, which requires several days to form a colony.

A naturally occurring genome may be removed from a cell by any method,for example, by lysis and digestion. In an exemplary embodiment, about10¹⁰ to about 10¹³ Mycoplasma cells grown in SP4 medium, in suspensionor adherent to flasks, are washed with electroporation buffer comprising8 mM HEPES with 272 mM sucrose at pH 7.4. The washed cells are added to2.5 mL of the electroporation buffer at 4° C., triturated to break upany cell clumps, and pelleted by centrifugation at 4,575 g for 10 min at4° C. The supernatant is decanted and the centrifuge tubes are invertedfor a few minutes to minimize residual supernatant. Cells areresuspended in 100 μL of electroporation buffer plus 10 percentglycerol, and mixed with an equal amount of 2 percent low-melting-pointagarose or agarose at about 56° C. The resulting cell suspension is castin rectangular blocks while the agarose is still in a liquid state. Eachblock, or “plug,” is then digested overnight at about 50° C. to 56° C.in 5 mL of proteinase K reaction cocktail (comprising 100 mMethylenediaminetetraacetic acid (EDTA) at pH 8.0, 0.2 percent sodiumdeoxycholate, 1 percent sodium lauryl sarcosine, 2 percent sodiumdodecyl sulfate, and 1 mg/mL proteinase K) per mL of plug. The plugs arethen washed with 30 min of agitation four times in a wash buffercomprising 20 mM Tris buffer at pH 8.0 and 50 mM EDTA. The wash bufferfor the second or third wash also comprises 1 mM phenylmethylsulfonylfluoride. A synthetic genome may also be handled in this manner beforeintroduction into a cell or cell-like system.

At this point the genomic DNA is relatively free of protein and othercytoplasmic components, and is suspended in agarose that protects itfrom shear and other forces that could fragment the genome during anysubsequent, optional rounds of dialysis in 8 mM HEPES with 272 mMsucrose at pH 7.4 or other handling. The genomic DNA optionally can besubjected to pulsed-field gel electrophoresis to separate intact fromfragmented genomes. Covalently closed circular genomes are relativelyimmobile in pulsed-field gel electrophoresis, while linear DNAmolecules, RNA, and any remaining peptides electrophorese out of theagarose plugs. Thus, after pulsed-field gel electrophoresis, the plugsare highly enriched for covalently closed circular duplex DNA genomes.The genome-containing agarose plugs can be removed from the pulsed-fieldgels and processed for introduction into cells or cell-like systems. Theexcised plugs can be dialyzed in 10 mM Tris buffer at pH 7.5, 1 mM EDTA,200 μM spermine (or other polyamine, such as polyethanolamine, or anucleoid condensation protein such as Dps) and 25 mM NaCl at roomtemperature for 30 min to further compact the DNA through screening ofits negative charges. The agarose may be digested with agarase,optionally after addition of 4 μg/mL low-molecular-weight poly-L-lysine,and commercial liposome-producing reagents may be added to yield amixture useful for introducing genomes into cells or cell-like systemsthrough transfection. A synthetic genome may also be handled in thismanner before introduction into a cell or cell-like system.

An alternative example of obtaining a naturally occurring genome from acell involves lysis and digestion in liquid rather than in agarose.After pelleting by centrifugation at 4,575 g for 10 min at 4° C., cellsare lysed by adding sodium dodecyl sulfate at a final concentration of 1percent. EDTA is added to a final concentration of 100 mM, RNase A isadded at 10 U/mL and the mixture is incubated at 37° C. for 30 min, andthen proteinase K is added at a concentration of about 20 to about 100μg/mL and the mixture is incubated at 55° C. for about 3 to about 16hours. The genomic DNA is then precipitated in 3 volumes of ethanol, theprecipitation vessel is rolled gently so that the DNA adheres to itswall, the liquid is removed, and the DNA is washed several times withcold 70 percent ethanol and once with TE buffer (comprising 10 mMTris-HCl at pH 7.4 and 1 mM EDTA). The ethanol/TE buffer is removed andthe DNA is dried, and then resuspended in TE buffer plus 5 percentsucrose. A synthetic genome may also be handled in this manner withminimal DNA breakage before introduction into a cell or cell-likesystem.

The introduced genome may be any genome, such as a naturally occurringgenome, a genome made with or without the aid of bioinformatics or othertheoretical or computational methods, or a hybrid or chimaera of one ormore naturally occurring and/or manmade genomes. For example, a clusterof genes occurring naturally in one or more organisms or organelles maybe inserted into the naturally occurring genome of a microorganism ororganelle, with or without the assistance of automated laboratoryequipment. In some embodiments, the introduced genome is a minimalgenome, such as the E. coli minimal genome or the M. genitalium minimalgenome.

In an exemplary embodiment, the genome is prepared by assemblinginterchangeable nucleic acid “cassettes” by any pathway. A cassette is anucleotide sequence of any length that is designed to comprise one ormore genes or gene fragments, and optionally one or more regulatory,structural, or experimental sequences. The genes included in a cassettemay be in any order (e.g., “shuffled” from a naturally occurring order),may occur multiple times, and may be incomplete or interrupted by othernucleic acid segments, such as genes or parts of genes. The nucleotidesequences included in a cassette may occur naturally, may be manmadewith or without automated or computer assistance, or be a hybrid of oneor more naturally occurring and one or more manmade sequences.

The introduced genome may comprise nucleic acid molecules of any kind.For example, the introduced genome may be composed of one or morestretches of one or more units of DNA (deoxyribonucleic acid), RNA(ribonucleic acid), or PNA (protein-nucleic acids), with or withoutmodified or substituted nucleotides. Modified or substituted nucleotidesinclude those that do not normally occur in biologically derived nucleicacid molecules, such as biotinylated nucleotides and nucleotides withaltered ring, phosphate or sugar moities. Nucleic acid molecules maycomprise genes, as well as nonencoding regions such as binding sites forone or more proteins or other materials, or sites designed forattachment to substrate, or for any other purpose. The introducednucleic acid molecules may be derived from any source, including cellsof animals, plants or protists including archaebacteria, viruses,subcellular organelles and/or chemical synthesis. The introduced nucleicacid molecules may be the result of ab initio design of proteins orenzymes that do not occur naturally, such as aminoacyl tRNA synthetasesfor non-standard amino acids. The nucleic acid molecules optionally maybe folded, supercoiled or otherwise compressed. In an exemplaryembodiment the introduced nucleic acid molecules are double-stranded,but single-stranded nucleic acid molecules or nucleic acid moleculeswith other geometries are encompassed by the provided invention.

Introduction of a genome may be performed by any means. For example, agenome or other nucleic acid molecule may be enclosed in or complexedwith either a liposome or a micelle, which may or may not also containother matter such as supporting protein molecules, a system fortranscription and translation, elemental ions, plastic or otherparticles and/or small molecular compounds. Then, the micelle orliposome containing or complexed with the genome may be contacted with atarget host cell under circumstances that promote the incorporation ofthe vesicle contents into the cell. Other methods for installation ofgenomes into recipient cells or cell-like systems include physicalapproaches such as: optical tweezers, magnet assisted transfection inwhich genomes to be introduced are bound to magnetic nanobeads and thenpulled into recipient cells by magnets, laser enhanced transformation,ballistic approaches in which the genomic DNA to be introduced iscomplexed with gold or tungsten nanoparticles and then blown at highvelocity into the recipient cells, and electroporation; chemical methodssuch as: polyethylene glycol mediated methods, introduction viasynthetic pores created in cells using cyclic peptides, calcium mediatedprecipitation of the DNA to be introduced onto the recipient cells withsubsequent incorporation, and lithium acetate mediated precipitation ofthe DNA; and biological approaches such as: simple application of theDNA in agar plugs to the recipient cells followed by DNA uptake,fusogenic peptides, and induction of natural competency.

In an exemplary embodiment, M. genitalium chromosomes containingantibiotic resistance markers (such as tetM) are introduced into one ormore M. genitalium or M. pneumoniae cells via lipofection (fusion of aliposome with a target cell to deliver the liposome contents into thetarget cell, described above). The one or more target cells are expectedto lack the antibiotic resistance marker, thus remaining sensitive totetracycline, to which the introduced genome is resistant. One day afterlipofection, tetracycline may be added to the growth medium for one ormore target cells, so that only the one or more target cells into whicha genome has been introduced will grow. It may be necessary to disablethe homologous recombination protein (RecA) of the recipient cells inorder to avoid the antibiotic resistance marker recombining into therecipient cells.

In another exemplary embodiment, genomic DNA from M. mycoides isisolated via digestion in agarose as described above. One or moreagarose plugs containing purified DNA are melted, mixed withpolyethylinimine and cationic liposomes (e.g., LIPOFECTAMINE™ 2000(Invitrogen)) and the genomic DNA is introduced into one or more M.capricolum cells via lipofection. In an exemplary embodiment, nakedgenomic DNA from Mycoplasma mycoides Large Colony is introduced into oneor more M. capricolum cells using a polyethylene glycol mediated method.

The genome may be introduced into a cell or a cell-like system.Exemplary embodiments include introducing a genome into a living plant,animal, fungal, yeast, mitochondrion, chloroplast, or other cell ororganelle, whether in vivo, in culture, or in other circumstances,introducing a genome into a cell from which the naturally occurringgenome has been removed, and/or introducing a genome into amembrane-bound volume derived by any method, such as a red blood cell ora manmade lipid vesicle in aqueous solution. For example, a genome maybe removed from an aquatic protist by lysis and digestion and introducedinto a ghost cell by electroporation (see also U.S. Provisional PatentApplication Ser. No. 60/752,965, cited above). Alternatively, the genomecontaining an antibiotic resistance gene or other selectable marker canbe introduced into a living plant, animal, fungal, yeast, mitochondrion,chloroplast, or other cell or organelle so that transiently the cell ororganelle contains both the introduced genome and its own genome.Subsequent cell or organelle division then segregates the introducedgenome into a new daughter cell or organelle. That cell or organellethen takes on the phenotype programmed by its introduced genome.

In some embodiments a synthetic cell is produced, which may or may notbe able to self-replicate. In an exemplary embodiment, a genome isintroduced to a cell which already contains a naturally occurringgenome, and the cell divides into two cells, one containing thenaturally occurring genome, and another containing the introducedgenome. Synthetic cells include the cell containing the introducedgenome, as well as other microorganisms recognizable as engineeredcells, for example, a cell from which the naturally occurring genome hasbeen removed and into which a different genome has been introduced.

In an exemplary embodiment, one or more synthetic cells capable ofreplication contain a genome designed to express one or more particulargene products under certain conditions. For example, the naturallyoccurring genome may be removed from an E. coli cell, and a genomeintroduced that comprises a minimal genome for E. coli in a known growthmedium and a cassette for expressing one or more therapeutic peptides,such as the insulin peptides. One or more of the altered, or synthetic,cells are cultured under conditions promoting their replication andexpression of the therapeutic peptide, which then may be collected. Oneskilled in the art will be able readily to determine conditionsappropriate for cell replication and expression of the one or moredesired gene products.

FIG. 1 is a diagram illustrating an exemplary method for installing agenome or partial genome into a cell or cell-like system. A genomeoutside of a cell may comprise, for example, naked DNA (not shown), orone or more supercoiled nucleic acid molecules 102 with one or morescaffolding proteins 104, or one or more supercoiled nucleic acidmolecules 102 with one or more scaffolding proteins 104 and one or moreribosomes 106 (not to scale), or one or more supercoiled nucleic acidmolecules 102 with one or more scaffolding proteins 104, one or moreribosomes 106, and one or more accompanying small molecules 108 and oneor more single-stranded nucleic acid molecules 110. One or more genomesmay be introduced into a membrane bound aqueous volume 112, such as alipid vesicle. In an exemplary embodiment, a genome comprising a minimalM. genitalium genome with cassettes added to produce a tomato proteinand with marker nucleotides added is introduced in an agar plug to an E.coli cell that still contains its naturally occurring genome.

FIG. 2 is a diagram illustrating an exemplary method for installing agenome or partial genome including supercoiled DNA 202, scaffoldingproteins 204 and ribosomes 206 (not to scale) into an E. coli cell 208that still contains its naturally occurring genome 210. In thisexemplary embodiment, the cell with two genomes divides along thehypothetical triple line in the diagram to produce a daughter cell withthe naturally occurring E. coli genome 210, and a synthetic daughtercell with the introduced genome 202. The daughter cells may furtherself-replicate.

FIG. 3 is a diagram illustrating an exemplary method for producing agene-expression product of interest using one or more synthetic cells.In an exemplary embodiment, a synthetic genome 302 comprises a naturallyoccurring genome removed from a natural cell into which a manmadecassette coding for a desired protein has been spliced. The genome 302is in the form of double-stranded, supercoiled DNA with scaffoldingproteins 304. The genome 302 is introduced into a ghost cell 306 using,for example, optical tweezers. One or more such synthetic cells 308 withsuch genomes 302 are prepared and plated on a growth medium 310 thatprovides the synthetic cells 308 with the ability to self-replicate,forming one or more colonies 312 and expressing the desired protein.

While various embodiments have been described above, it should beunderstood that they have been presented by way of example only, and notlimitation. For example, any other set of endonuclease reactioncomponents that achieves the provided method may be used. Thus, thebreadth and scope of a preferred embodiment should not be limited by anyof the above-described exemplary embodiments.

1. A method for making a synthetic cell, the method comprising:obtaining a genome that is not within a cell; and introducing the genomeinto a cell or cell-like system.
 2. The method of claim 1 whereinintroducing the genome further comprises introducing the genome into acell containing a genome, and further comprises allowing the cell todivide into a daughter cell with the naturally occurring genome of theparent cell, and a synthetic daughter cell with the introduced genome.3. The method of claim 1 wherein introducing the genome furthercomprises introducing the genome from a cell of one species into a cellof a different species.
 4. The method of claim 1 wherein the genomecomprises naked DNA.
 5. The method of claim 1 wherein the genomecomprises a naturally occurring genome.
 6. The method of claim 1 whereinthe genome comprises a manmade genome.
 7. The method of claim 1 whereinthe genome comprises a hybrid genome comprising one or more naturallyoccurring components and one or more manmade components.
 8. The methodof claim 1 wherein the genome comprises one or more nucleic acidsequences providing one or more features other than a genetic sequence.9. The method of claim 1 wherein the genome comprises a minimal genome.10. The method of claim 1 wherein the genome is a partial genome,comprising one or more chromosomes or chromosome fragments.
 11. Themethod of claim 1 wherein the cell-like system comprises amembrane-bound volume.
 12. The method of claim 1 wherein the cell-likesystem comprises a lipid vesicle.
 13. The method of claim 1 wherein thecell-like system comprises a cell from which one or more intracellularcomponents has been removed.
 14. The method of claim 1 wherein thecell-like system comprises a cell from which the genome has beenremoved.
 15. The method of producing a product of interest, comprisingculturing one or more synthetic cells produced by the method of claim 1under conditions effective to produce the product.
 16. A synthetic cellproduced by obtaining a genome that is not within a cell, andintroducing the genome into a cell or cell-like system.
 17. Thesynthetic cell of claim 16 wherein the obtained genome is a partialgenome, comprising one or more chromosomes or chromosome fragments. 18.The synthetic cell of claim 16 wherein the genome is obtained from acell of one species and introduced into a cell of another species.